Effect of atomic charge,solvation, entropy,and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

The molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and MM-generalized-Born surface area (MM-GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM-PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM-PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO-3G and B3LYP/cc-pVTZ), (ii) the MM-GBSA approach over MM-PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer-aided drug design. © 2012 Wiley Periodicals, Inc.     

On stability and protonation of multielectron systems: The concept of proton affinity. II. Dissociative proton attachment and protonation—Deprotonation mapping

A few touches on the thematic palette “molecular protonation” directly linked to the concept of molecular stability have been accomplished. They are of different nature, of different origin, and taken from “different angles” of lighting; however, together, they definitely provide a sufficiently complete picture “The protonation interaction, as being strong enough, may break the stability of molecules subject to protonation.” © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A counterintuitive structural effect of metal-metal bond protonation and its electronic underpinnings

Protonation across the metal-metal bond in the complexes [(CO)(2)M(mu-dppm)(mu-PtBu(2))(mu-H)M(CO)(2)] (M=Fe or Ru, dppm=Ph(2)PCH(2)PPh(2)) induces M-M bond shortening of up to about 0.05 A. DFT calculations on simplified iron models reproduce this trend well. Conversely, the computations show that the M-M distance in the dimer [{Cp*Ir(CO)}(2)] lengthens with two consecutive protonations, but there are no crystal structure determinations to highlight the effects on the Ir-Ir bond. DFT calculations and the analogous cobalt system confirm that the transformation of a two-electron, two-center (2e-2c) bond into a 2e-3c bond is accompanied by the predicted elongation. An MO analysis indicated similar nature and evolution of the M-M bonding these cases. In particular, the HOMOs of the mono-hydrido cations [Cp(CO)M(mu-H)M(CO)Cp](+) (M=Ir, Co) have evident M-M bent-bond character, and hence subsequent protonation invariably causes a decrease in the bond index. The Fe(2) and Co(2) systems have also been analyzed with the quantum theory of atoms in molecules (QTAIM) method, but in no case was an M-M bond critical point located unless an artificially shorter M-M distance was imposed. However, the trends for the atoms-in-molecules (AIM) bond delocalization indexes delta(M-M) confirm the overall M-M bond weakening on protonation. In conclusion, all the computational results for the iron system indicate that the paradigm of a direct correlation between bond strength and distance is not always applicable. This is attributable to a very flat potential energy surface and various competing effects imposed by the bridging ligands.     

Boratabenzene Anions C5B(CN)6− and C5B(CF3)6− and the Superacidic Properties of their Conjugate Acids

Designing superacids: A computational study of protonated boratabenzenes and the gas‐phase acidity of their conjugate acids is presented. Conjugate acids of boratabenzenes substituted with CN or CF₃ groups (see figure) are highly acidic species; the protonated hexacyanoboratabenzene and hexakis(trifluoromethyl)boratabenzene have computational gas‐phase acidities of 250.5 and 276.8 kcal mol^?1, respectively.

     

Ag/质子化g-C3N4纳米棒材料的制备及其光催化降解性能

制备了 Ag 负载于质子化 g-C₃N₄(pCN)的纳米棒材料(Ag/pCN),对比了 g-C₃N₄(CN)、表面负载 Ag 的 CN(Ag/CN)、pCN 和 Ag/pCN在可见光条件下光催化降解亚甲蓝(MB)溶液的效果。结果表明,Ag/pCN光催化效率最高(92.63%),并且具有良好的稳定性;通过光电流-时间(I-t)曲线、Nyquist曲线、Mott-Schokkty曲线和捕获实验探究了Ag/pCN光催化降解MB的机理：虽然pCN的π共轭体系较CN发生变化,但由于形成了纳米棒,其比表面积的增加以及Ag负载的协同效应致使Ag/pCN具有优异的光催化性能。光催化过程中羟基自由基(·OH)是起主要作用的活性物质,其由光生电子(e^-)与表面吸附的 O₂反应产生以及光生空穴(h⁺)与H₂O或OH^-反应产生。